Category Archives: Data Review

Tip for Optimizing the Speed of Processing Data for TraceFinder 4.0 and later

TraceFinder 4.0 introduced the ability to perform target analysis on peptide sequences. Given that these chemical analysis methods can be very long (i.e. 3hours for a single sample) and have drastically shifting retention times between samples, TF 4.0 introduced the Extraction Time Window as a peak detection setting.

This new setting allows the user to set a window around where the peak might elute. The default setting is 3 minutes, which means +/- 1.5 minutes from the expected retention time.

This setting may be a bit wide for stable chromatography. A typical setting for the Extraction Time Window is 1 minute or +/- 30 seconds from the expected retention time. This setting can be changed in the Master Method Template or the Local Method.  This new setting can then be pushed to all the compounds with two mouse clicks or can be optimized for each target peak, clicking the Three Lined Button in the right coner of the settings page and selecting “Apply current extraction window settings to all peaks in the method

Since the amount of data being extracted for the targeted peak is reduced, the amount of time per peak analysis is reduced. This setting is separate from the Peak Detection and View Width Window under the Retention Times Tab.


Peak Extraction Window

How to use the Threshold Sample in Comparative View

To utilize comparative view to its fullest, one must set 3 three properties.

  • Method-Limits-Threshold setting – this setting allows the user to set the height of the horizontal threshold bar in data review. There are two settings.
    1. Threshold – a fixed peak height amount
    2. % of Threshold the Sample – dynamic threshold according the peak height of the specified Threshold sample, as described below.

Method Threshold Setting

  • Batch view-samples-groups column – this setting assigns samples to groups that are displayed horizontally in the comparative view peaks panel. A unique alpha numeric symbol is used to assign a sample to a group. Each sample with the same symbol is a member of that group. The samples are shown side by side in the peak review panel and are ordered left to right by descending order in the sample grid above.Batchview Threshold Setting
  • Batch view-threshold samples – the setting allows the user to assign a threshold sample for each group. Any member of the group can be set as the threshold sample. However, only one sample can be utilized at a time in the group. If you want one particular sample to be used as the threshold across the batch make sure it is a member of all the group. For example if you used numbers for the group name and you have 10 groups, the entry for this sample in the groups column would be 1,2,3,4,5,6,7,8,9,10.Threshold sample selection

The settings in the examples above allow for the display shown below.

The tall red vertical bar marks the expected retention time and the smaller vertical bars are the edges of the retention time window. Both set in the method parameters for each compound. This allows you to see the drift of chromatography within the sample group. The horizontal red line is the threshold as set in the method as a fixed amount or relative percentage of the threshold sample, as set in the method.

Comparative View in Data Review

A point to note, there were a few instances where everything was setup properly but nothing displayed in the Comparative view. It was found that some older  video drivers not comply with technologies Microsoft used to render the images in this complex grid. However, the issue was fixed in all cases by updating to the latest video drivers for the PC.

TF 3.2 Setting up to Data Review to display Positive results first

In the video below, we have set up the flagging criteria to be able to sort and float Positive results, above the LOR/Cutoff Limit set in the method settings,to the top of the data review grid. We have also setup a flag to allow compounds with detected peaks but fall under the LOR/Cuttoff level in the QAQC section of the master/local method, to appear below the positive results. This should assist in labs wanting to review data by exception and to validate their data review process to incorporate into their SOPs to utilize this criteria.

The Power of Comparing – Do these things go together? – TF 3.1: The NEW Comparative View in Data Review

Many have asked us, how to easily compare compound response across multiple samples.

Here is the answer.

Comparative View allows for a group of samples to be shown side by side with fixed Y-scale to the most intense or a selected threshold reference sample.

The view allows the user to visualize the Expected Retention Time and the Range of Time for peak detection via Markers. This will clearly indicate how the chromatography is responding.

The user can designate samples to be part of individual or multiple groups, by assigning alpha-numeric characters to column in the sample definition screen. Once assigned, and a member of the group is selected in the results grid, the multi-chromatogram pane will display the sample group in columns and the compounds in rows.

The use of a Threshold Sample and a new tab in the method under the Limits section, allows for a visual bar to be set for a specific peak height or a percentage of the Threshold Sample’s peak height.

Below is a video of the new feature in TraceFinder 3.1, debuting at ASMS 2013.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

Applying an external/historical curve to a batch of samples after Acquisition – Ask A Guru

The video below shows how to apply a calibration curve from one batch that contains calibration samples to a batch of samples that contain no calibrators.

This workflow is the same as selecting the external curve in the Acquisition workflow, but may be used on any batch of samples after acquisition.

The features allows the user to run a calibration batch in the morning and use that curve for all subsequent batches for the time period their SOP allows.

HMMMMMM… Maybe your day just got alittle easier.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

TF3.0 – Using Estimated/Semi-Quan Amounts

In certain parts of TraceFinder and LabForms, we had exposed the ability to use estimated amounts of substances that did not have their own calibration curve. This feature goes back to the days of the Incos data systems, circa 1980.

In TF 3.0 we have exposed this capability, to be a bit more friendly to use and to be interactive in the user interface, versus just report generated.

In the following video, you will see where to set a compound to use the estimated feature and how it is displayed throughout the applications with visual clues to help you determine that the results you are observing is a semi-quantitative amount.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

TF 3.0 has some new homes for some functions previously available

Part of the process of looking at User Interface changes, is being able to make sure that we present a logical way of navigating to things, that we may not use on a regular basis. This makes it easier for the end user to remember where to get to that special function, when they need it.

So in the application we still have many right click options, but we have also moved many of the scattered functions into the menu drop downs.

These changes have come from customer request or questions about where functions are.

So here are the most used functions that are not directly data linked.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

TF 3.0 Export Results Grid to Excel and Copy Images to Clip Board

Sticking to new features in data review, we’ll continue with a simple workflow.

One of the many request that TraceFinder has received over the last year has been to have the ability to export the results grid directly to Excel instead of having a Custom Report generated.

In TF 3.0 all data grid results whether in the quantitative views or targeted screening section, export all data to Excel or CSV files directly.

No need to produce a custom report and navigate through the files menus to go get it.

Simply export and place the file where you want it.

Also a feature that has been requested is the ability to copy high definition images of chromatograms and such to the clipboard for use in papers, lab notebooks and presentations/posters.

We also did this in TF 3.0

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.


New TF 3.0 Targeted Screening Workflow in Data Review (or the marriage of TF and ExactFinder)

A new feature to TraceFinder 3.0 is targeted screening. The workflow and method setup that were included in ExactFinder has been included in TraceFinder 3.0. Though it has been expanded to support Nominal Mass as well as HRAM.

That means this feature will work for all mass spectrometers from the GC single quads to the Q-Exactive.

Though some sections are more geared for HRAM, they can just not be used when using nominal mass data.

The other aspect is that TF gives you the ability to acquire, process and report on the fly during acquisition. Therefore, if you so choose you don’t have to wait to review your data. So this expands the capabilities that was introduced in ExactFinder.

This is our first step with this functionality and more is to come in following releases, but there are some interesting things that can be done by having these two workflows combined.

Again the video is a little longer that my 2 minute rule but there is a lot to look forward to.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.

New TraceFinder 3.0 Data Review Elements

In TraceFinder 3.0, you will find that we have changed the Graphical User Interface quite a bit. Other than changing some of the colors and the navigation style we have also added elements to help review data in a way that can be tailored.

A concept that came across to our team was to help tell the story of the data. This is what TraceFinder was intended to do from its concept. We realized that many scientist that will use this and related products will not be “CLASSICAL” mass spec people. Young new chemist or other scientist not use to mass spec data moving into the lab need to be able to see what they need to know about the data and have a feel on what works best for them. At the end of the day they are telling the story of the data to their customers.

Our concept is to give you the ability to choose what you want to see and how you want to see it.

In forthcoming releases you will have the ability to “Read the Cliff Notes” of the data or the other end of the spectrum of reading “War and Peace,” if you so choose. We don’t want to limit the data or have the data be so overwhelming it can’t make sense.

So in this video we will show you how to navigate in the Compound and Sample Views which are just different ideas on how to look at the data. Also how to arrange the views so it makes sense, or makes it easier to read through the data.

A big plus is the ability to filter out data you don’t care to see or only data you are interested in.

All this and the views are remembered automatically when a User signs out or closes the application.

Although the video only takes place on one screen. Any part of the data review section is a dockable panel so you can have parts on multiple monitors and they will remain synced. I personally use a three monitor setup and have a multipeak panel on one, a detailed view on another and my data review grid on my main display.

Remember we can only make it better if we hear back from you so, please send in your ideas, comments or questions. The video is a little longer than my 2 minute rule but it should explain a lot of the NEW ELEMENTS and their functions.

If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.